This repository contains Python scripts to ingest and process data for mutational signature analysis, from public datasets in the International Consortium for Cancer and Genomics (ICGC) Data Portal, with an emphasis on adherence to FAIR (Findable, Accessible, Interoperable, and Reusable) principles.
The jupyter notebook notebooks/Consuming ICGC Data.ipynb shows how to consume simple somatic mutation data from the ICGC Data Portal via its APIs.
The jupyter notebook notebooks/Processing ICGC Data.ipynb shows how to process the simple somatic mutation (SSM) data that we downloaded from the ICGC Data Portal. After processing the SSM dataset, we generate a mutational spectra matrix, which tallies the counts for each context (as determined by the base on the 5' and the 3' ends of the mutated allele) of single base substitution. To obtain the context of the substitution, we require the GRCh37 reference genome. We obtain this genome via the UCGC Genome Browser API. The mutational spectra matrix for the BRCA datasets is stored in data/mutational_spectra_wgs/. This dataset can be readily used for mutational signature analysis.
The jupyter notebook notebooks/Simulating MSK-IMPACT 410.ipynb shows how to simulate a mutational spectra from MSK-IMPACT 410 gene panel from the MAF files generated from the ICGC SSM whole genome analysis dataset.
The jupyter notebook notebooks/Consuming and Preparing MSK-IMPACT Data.ipynb shows how to use the cBioPortal web API to download MSK-IMPACT data from the 2017 paper: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. The downloaded data is then converted into a mutational spectra matrix and stored at data/msk_impact_nature_2017/.